TY - JOUR
T1 - Global quantitative proteomics reveals novel factors in the ecdysone signaling pathway in Drosophila melanogaster
AU - Sap, Karen A.
AU - Bezstarosti, Karel
AU - Dekkers, Dick H.W.
AU - van den Hout, Mirjam
AU - van Ijcken, Wilfred
AU - Rijkers, Erikjan
AU - Demmers, Jeroen A.A.
N1 - Publisher Copyright: © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
PY - 2015/2/1
Y1 - 2015/2/1
N2 - The ecdysone signaling pathway plays a major role in various developmental transitions in insects. Recent advances in the understanding of ecdysone action have relied to a large extent on the application of molecular genetic tools in Drosophila. Here, we used a comprehensive quantitative SILAC MS-based approach to study the global, dynamic proteome of a Drosophila cell line to investigate how hormonal signals are transduced into specific cellular responses. Global proteome data after ecdysone treatment after various time points were then integrated with transcriptome data. We observed a substantial overlap in terms of affected targets between the dynamic proteome and transcriptome, although there were some clear differences in timing effects. Also, downregulation of several specific mRNAs did not always correlate with downregulation of their corresponding protein counterparts, and in some cases there was no correlation between transcriptome and proteome dynamics whatsoever. In addition, we performed a comprehensive interactome analysis of EcR, the major target of ecdysone. Proteins copurified with EcR include factors involved in transcription, chromatin remodeling, ecdysone signaling, ecdysone biosynthesis, and other signaling pathways. Novel ecdysone-responsive proteins identified in this study might link previously unknown proteins to the ecdysone signaling pathway and might be novel targets for developmental studies. To our knowledge, this is the first time that ecdysone signaling is studied by global quantitative proteomics. All MS data have been deposited in the ProteomeXchange with identifier PXD001455 (http://proteomecentral.proteomexchange.org/dataset/PXD001455).
AB - The ecdysone signaling pathway plays a major role in various developmental transitions in insects. Recent advances in the understanding of ecdysone action have relied to a large extent on the application of molecular genetic tools in Drosophila. Here, we used a comprehensive quantitative SILAC MS-based approach to study the global, dynamic proteome of a Drosophila cell line to investigate how hormonal signals are transduced into specific cellular responses. Global proteome data after ecdysone treatment after various time points were then integrated with transcriptome data. We observed a substantial overlap in terms of affected targets between the dynamic proteome and transcriptome, although there were some clear differences in timing effects. Also, downregulation of several specific mRNAs did not always correlate with downregulation of their corresponding protein counterparts, and in some cases there was no correlation between transcriptome and proteome dynamics whatsoever. In addition, we performed a comprehensive interactome analysis of EcR, the major target of ecdysone. Proteins copurified with EcR include factors involved in transcription, chromatin remodeling, ecdysone signaling, ecdysone biosynthesis, and other signaling pathways. Novel ecdysone-responsive proteins identified in this study might link previously unknown proteins to the ecdysone signaling pathway and might be novel targets for developmental studies. To our knowledge, this is the first time that ecdysone signaling is studied by global quantitative proteomics. All MS data have been deposited in the ProteomeXchange with identifier PXD001455 (http://proteomecentral.proteomexchange.org/dataset/PXD001455).
KW - Developmental pathway
KW - Dynamic proteome
KW - Ecdysone signaling
KW - SILAC
KW - Systems biology
KW - Transcriptome
UR - http://www.scopus.com/inward/record.url?scp=84922931260&partnerID=8YFLogxK
U2 - https://doi.org/10.1002/pmic.201400308
DO - https://doi.org/10.1002/pmic.201400308
M3 - Article
C2 - 25403936
SN - 1615-9853
VL - 15
SP - 725
EP - 738
JO - PROTEOMICS
JF - PROTEOMICS
IS - 4
ER -